As a first step, you need to upload a sequence file in FASTA format. This is the sequence you can search using PatScan. The file will be kept on the server as long as you work on it and deleted an hour after you finished using the software.
Once your file is uploaded, you can specify a pattern by dragging pattern elements from the menu bar on the right side of the screen to the work area. Once the pattern element is on the work area, you can fill in details, and reorder the elements by dragging them around.
Above the pattern area, there is a configuration menu containing a couple of buttons to adjust the software.
The DNA/Protein selector allows you to tell PatScan what kind of sequence file you uploaded. This affects the selection of available pattern elements.
While working on the pattern, you can switch on the continuous preview, that will regularly search your uploaded sequence for the currently selected pattern. This will allow you to tweak the pattern until you get the desired result.
If you want to get rid of the current pattern elements, you can clear all of them using the clear button. Alternatively, you may drag single elements onto the trash on the right hand menu.
If you want to get an example of many of the possible pattern elements, you can load an example.
Below the work area, you can expand the computed pattern view, in case you need to tweak the generated pattern manually
or pick one of the following provided genomes: